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BGI Team Developing 'All-in-One' Capture Technique to Go Beyond the Exome


By Monica Heger

This story, originally published on Nov. 16, has been updated to include information about the MHC capture technique BGI has developed with Roche NimbleGen.

SHENZHEN, China — BGI executive director Wang Jun said last week that researchers at the institute are developing a capture technique that will enrich for the whole exome, regulatory regions, the major histocompatibility complex locus, and population-based tag SNPs.

Wang described the technology last week at the International Conference on Genomics hosted by BGI.

The technique, dubbed All-in-One, will capture between five and 10 percent of the genome, which will offer a lower-cost solution than whole-genome sequencing, while still capturing more information than exome sequencing. "We still cannot afford to sequence whole human genomes for many samples," Wang told In Sequence.

He said the team is developing its own pull-down solution because at only one to two percent of the genome, "the exome is not enough." While exome sequencing captures the gene-coding regions, "lots of functional regions in the genome are non-coding," explained Wang. The All-in-One approach captures those regions.

The MHC region is particularly important for disease, he said. In addition, being able to capture population-specific variation will be particularly important for studying complex diseases, which may have genetic differences between ethnicities.

"The variation spectrum is quite different in different populations," said Wang, with some sequences being so specific that they can be classified as "yes or no variation" across populations.

Wang said that BGI researchers have already tested the capture technique in Chinese samples for complex disorders. "Once you have a [population-specific] reference genome," he said, this capture technique will "allow you to re-sequence more samples based on the reference."

BGI also recently announced that it has developed in collaboration with Roche NimbleGen a capture technique for the MHC region based on NimbleGen's SeqCap EZ Choice Library. The capture technique targets a 4.97 megabase region on the short arm of chromosome 6, which includes the traditional 3.37 megabase MHC region, as well as 1.6 megabases of surrounding MHC.

The capture region includes 150 expressed genes and eight known haplotypes and enables targeted sequencing of 97 percent or more of the overall MHC region, with close to 100 percent coverage of the gene-coding regions, Hui Jiang, associate director of the science and technology department at BGI, said in a statement.

Additionally, Wang said BGI researchers will design a pull-down solution pull-down for complex disorders.

Both the MHC specific capture technique and the pulldown for complex disorders will be developed first for internal use, and then for collaboration projects, Wang said.

Have topics you'd like to see covered by In Sequence? Contact the editor at mheger [at] genomeweb [.] com.